[petsc-users] Question about HDF5 Viewer and Datasets

[Matthew Knepley]

On Tue, Jun 23, 2020 at 8:56 AM Lucas Banting <bantingl at myumanitoba.ca>
wrote:

> Hello,
>
> I am trying to use the HDF5 viewer to store the solution of my system at
> every iteration.
> I am storing the solutions in order to compare two different results, one
> from an old sequential program and one from a new parallel program that is
> parallelized using the DMDA structure.
> I am using matlab to compare the results.
>
> In the sequential program, the vector for the solution is just a simple
> one dimensional vector made from VecCreate. In the parallel program, the
> vector is made from DMCreateGlobalVector.
>
> In both versions of the program, I create the viewer as:
>
> call PetscViewerHDF5Open(PETSC_COMM_WORLD,"filename.hdf5",&
>                         FILE_MODE_WRITE,hdf5viewer,ierr)
>
> When I load the files into MATLAB after words, the sequential program
> creates a new dataset each iteration, while the parallel version using
> DMCreateGlobalVector only stores a single dataset.
> Is there a way I can force both viewers to create a new dataset in the
> same way each time vecview is called? Or is there someway I can manually
> create a new dataset?
>

You can see inside the file using 'h5ls' and 'h5dump'. I believe that the
Vec is stored in HDF5 using the name (of the PetscObject). I think
that is happening is that you are not setting the name, which means it
defaults to the pointer, and that pointer is the same for your
global vector. I believe if you change the name at each iteration, they
will all be saved. You can also use the Timestep mechanism as Barry
suggests.

  Thanks,

     Matt


> I am using Open MPI 3.1.4, Petsc 3.12.4, Intel Fortran 2019.5, and hdf5/
> 1.10.5.
>
> Thanks,
>
> Lucas Banting
>
>

-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener

https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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